.. _ggd-show-env:

ggd show-env
============

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:code:`ggd show-env` is a tool used to show the ggd data package environment variables created during package installation
for the current conda environment.

During installation, ggd will place the processed files in a specific location on your system. To access
these files ggd creates up to two environment variables for each data package within a specific conda environment. 
These variables contain either the directory path to the processed files or the file path to the main data file. 
You can use :code:`ggd get-files` or :code:`ggd pkg-info` to find additional file paths for a ggd data
package, however, these environment variables provide quick access to the processed files without having to know
the file paths.

For details on using these environment variables in your analysis scripts see: :ref:`Using installed data <using-installed-data>`.


Using ggd show-env
------------------
You can use ggd show-env to get a list of ggd data package environment variables.
Running :code:`ggd show-env -h` will give you the following message:

show-env arguments:

+------------------------+-------------------------------------------------------------------------------------+
| ggd show-env           | Display the environment variables for data packages installed in the current        |
|                        | conda environment                                                                   |
+========================+=====================================================================================+
| ``-h``, ``--help``     | show this help message and exit                                                     |
+------------------------+-------------------------------------------------------------------------------------+
| ``-p``, ``--pattern``  | (Optional) Regular expression pattern to match the name of the variable desired     |
+------------------------+-------------------------------------------------------------------------------------+


Additional argument explanation: 
++++++++++++++++++++++++++++++++

There are no required arguments for using :code:`ggd show-env`, however, you can refine the results using
the :code:`-p` flag.

.. note:: 

   Environment variables ending with `_dir` point to the directory path of the installed data package.
   
   Environment variables ending with `_file` point to the main file from the installed data package. 


Examples
--------

1. Using ggd show-env
+++++++++++++++++++++

.. code-block:: bash

    $ ggd show-env

      *****************************

      Active environment variables:
      > $ggd_hg19_repeatmasker_ucsc_v1_dir
      > $ggd_hg19_repeatmasker_ucsc_v1_file
      > $ggd_grch37_esp_variants_ensembl_v1_dir
      > $ggd_grch37_esp_variants_ensembl_v1_file
      > $ggd_hg38_repeatmasker_ucsc_v1_dir
      > $ggd_hg38_repeatmasker_ucsc_v1_file
      > $ggd_grch37_reference_genome_ensembl_v1_dir
      > $ggd_grch37_reference_genome_ensembl_v1_file
      > $ggd_hg19_phastcons_ucsc_v1_dir
      > $ggd_hg19_phastcons_ucsc_v1_file
      > $ggd_hg19_gaps_ucsc_v1_dir
      > $ggd_hg19_gaps_ucsc_v1_file
      > $ggd_hg38_simplerepeats_ucsc_v1_dir
      > $ggd_hg38_simplerepeats_ucsc_v1_file
      > $ggd_hg19_simplerepeats_ucsc_v1_dir
      > $ggd_hg19_simplerepeats_ucsc_v1_file
      .
      .
      .

      *****************************

2. Using the `-p` flag
++++++++++++++++++++++

.. code-block:: bash

    $ ggd show-env -p ggd_hg19

      *****************************

      Active environment variables:
      > $ggd_hg19_phastcons_ucsc_v1_dir
      > $ggd_hg19_phastcons_ucsc_v1_file
      > $ggd_hg19_gaps_ucsc_v1_dir
      > $ggd_hg19_gaps_ucsc_v1_file
      > $ggd_hg19_repeatmasker_ucsc_v1_dir
      > $ggd_hg19_repeatmasker_ucsc_v1_file
      > $ggd_hg19_simplerepeats_ucsc_v1_dir
      > $ggd_hg19_simplerepeats_ucsc_v1_file
      .
      .
      .

      *****************************